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- EMDB-14547: Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for m... -

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Entry
Database: EMDB / ID: EMD-14547
TitleStructure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation
Map data
Sample
  • Complex: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
    • Protein or peptide: Cullin-7
    • Protein or peptide: F-box/WD repeat-containing protein 8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: S-phase kinase-associated protein 1
  • Ligand: ZINC ION
KeywordsCullin-RING Ubiquitin E3 Ligase / LIGASE
Function / homology
Function and homology information


3M complex / F-box domain binding / anaphase-promoting complex / PcG protein complex / XBP1(S) activates chaperone genes / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation of dendrite morphogenesis / cellular response to chemical stress ...3M complex / F-box domain binding / anaphase-promoting complex / PcG protein complex / XBP1(S) activates chaperone genes / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / positive regulation of dendrite morphogenesis / cellular response to chemical stress / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / positive regulation of protein autoubiquitination / protein neddylation / labyrinthine layer blood vessel development / NEDD8 ligase activity / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / Cul4A-RING E3 ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / regulation of mitotic nuclear division / negative regulation of type I interferon production / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / Prolactin receptor signaling / Golgi organization / cullin family protein binding / mitotic cytokinesis / cilium assembly / protein monoubiquitination / epithelial to mesenchymal transition / ubiquitin-like ligase-substrate adaptor activity / vasculogenesis / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / regulation of cellular response to insulin stimulus / positive regulation of TORC1 signaling / centriole / negative regulation of insulin receptor signaling pathway / post-translational protein modification / T cell activation / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Vpu mediated degradation of CD4 / cellular response to amino acid stimulus / placenta development / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Recognition of DNA damage by PCNA-containing replication complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / negative regulation of canonical Wnt signaling pathway / Iron uptake and transport / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / RING-type E3 ubiquitin transferase / beta-catenin binding / Degradation of beta-catenin by the destruction complex / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / NOTCH1 Intracellular Domain Regulates Transcription / Formation of TC-NER Pre-Incision Complex / microtubule cytoskeleton organization / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / Dual incision in TC-NER / Regulation of RAS by GAPs / protein polyubiquitination / positive regulation of protein catabolic process / Gap-filling DNA repair synthesis and ligation in TC-NER / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / cellular response to UV / KEAP1-NFE2L2 pathway
Similarity search - Function
: / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. ...: / : / : / CUL7/CUL9, N-terminal beta-barrel domain / CUL7/CUL9 ARM repeat domain / CPH domain / Mouse development and cellular proliferation protein Cullin-7 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / A Receptor for Ubiquitination Targets / F-box domain profile. / F-box-like domain superfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / : / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin family / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Quinoprotein alcohol dehydrogenase-like superfamily / SKP1/BTB/POZ domain superfamily / Galactose-binding-like domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-type fold / Ribosomal protein L2, domain 2 / Zinc finger, RING/FYVE/PHD-type / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RBX1 / S-phase kinase-associated protein 1 / Cullin-7 / F-box/WD repeat-containing protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHopf LVM / Schulman BA
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)789016European Union
Max Planck Society Germany
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structure of CRL7 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation.
Authors: Linus V M Hopf / Kheewoong Baek / Maren Klügel / Susanne von Gronau / Yue Xiong / Brenda A Schulman /
Abstract: Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). ...Most cullin-RING ubiquitin ligases (CRLs) form homologous assemblies between a neddylated cullin-RING catalytic module and a variable substrate-binding receptor (for example, an F-box protein). However, the vertebrate-specific CRL7 is of interest because it eludes existing models, yet its constituent cullin CUL7 and F-box protein FBXW8 are essential for development, and CUL7 mutations cause 3M syndrome. In this study, cryo-EM and biochemical analyses reveal the CRL7 assembly. CUL7's exclusivity for FBXW8 among all F-box proteins is explained by its unique F-box-independent binding mode. In CRL7, the RBX1 (also known as ROC1) RING domain is constrained in an orientation incompatible with binding E2~NEDD8 or E2~ubiquitin intermediates. Accordingly, purified recombinant CRL7 lacks auto-neddylation and ubiquitination activities. Instead, our data indicate that CRL7 serves as a substrate receptor linked via SKP1-FBXW8 to a neddylated CUL1-RBX1 catalytic module mediating ubiquitination. The structure reveals a distinctive CRL-CRL partnership, and provides a framework for understanding CUL7 assemblies safeguarding human health.
History
DepositionMar 17, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14547.png

Downloads & links

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Map

FileDownload / File: emd_14547.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å		0.85 Å/pix.
x 384 pix.
= 326.861 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8512 Å
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Contour LevelBy AUTHOR: 0.0129
Minimum - Maximum-0.02152804 - 0.06922655
Average (Standard dev.)0.000057327103 (±0.0018496583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.86078 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14547_msk_1.map
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Additional map: #1

Fileemd_14547_additional_1.map
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Half map: #1

Fileemd_14547_half_map_1.map
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Half map: #2

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Sample components

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Entire : Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex

EntireName: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
Components
  • Complex: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
    • Protein or peptide: Cullin-7
    • Protein or peptide: F-box/WD repeat-containing protein 8
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1
    • Protein or peptide: S-phase kinase-associated protein 1
  • Ligand: ZINC ION

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Supramolecule #1: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex

SupramoleculeName: Structure of the CUL7-RBX1-FBXW8-SKP1 cullin-RING ligase complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cullin-7

MacromoleculeName: Cullin-7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 191.564359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMVGELRYR EFRVPLGPGL HAYPDELIRQ RVGHDGHPEY QIRWLILRRG DEGDGGSGQV DCKAEHILLW MSKDEIYANC HKMLGEDGQ VIGPSQESAG EVGALDKSVL EEMETDVKSL IQRALRQLEE CVGTIPPAPL LHTVHVLSAY ASIEPLTGVF K DPRVLDLL ...String:
GPMVGELRYR EFRVPLGPGL HAYPDELIRQ RVGHDGHPEY QIRWLILRRG DEGDGGSGQV DCKAEHILLW MSKDEIYANC HKMLGEDGQ VIGPSQESAG EVGALDKSVL EEMETDVKSL IQRALRQLEE CVGTIPPAPL LHTVHVLSAY ASIEPLTGVF K DPRVLDLL MHMLSSPDYQ IRWSAGRMIQ ALSSHDAGTR TQILLSLSQQ EAIEKHLDFD SRCALLALFA QATLSEHPMS FE GIQLPQV PGRVLFSLVK RYLHVTSLLD QLNDSAAEPG AQNTSAPEEL SGERGQLELE FSMAMGTLIS ELVQAMRWDQ ASD RPRSSA RSPGSIFQPQ LADVSPGLPA AQAQPSFRRS RRFRPRSEFA SGNTYALYVR DTLQPGMRVR MLDDYEEISA GDEG EFRQS NNGVPPVQVF WESTGRTYWV HWHMLEILGF EEDIEDMVEA DEYQGAVASR VLGRALPAWR WRPMTELYAV PYVLP EDED TEECEHLTLA EWWELLFFIK KLDGPDHQEV LQILQENLDG EILDDEILAE LAVPIELAQD LLLTLPQRLN DSALRD LIN CHVYKKYGPE ALAGNQAYPS LLEAQEDVLL LDAQAQAKDS EDAAKVEAKE PPSQSPNTPL QRLVEGYGPA GKILLDL EQ ALSSEGTQEN KVKPLLLQLQ RQPQPFLALM QSLDTPETNR TLHLTVLRIL KQLVDFPEAL LLPWHEAVDA CMACLRSP N TDREVLQELI FFLHRLTSVS RDYAVVLNQL GARDAISKAL EKHLGKLELA QELRDMVFKC EKHAHLYRKL ITNILGGCI QMVLGQIEDH RRTHRPINIP FFDVFLRYLC QGSSVEVKED KCWEKVEVSS NPHRASKLTD HNPKTYWESN GSAGSHYITL HMRRGILIR QLTLLVASED SSYMPARVVV CGGDSTSSLH TELNSVNVMP SASRVILLEN LTRFWPIIQI RIKRCQQGGI D TRIRGLEI LGPKPTFWPV FREQLCRHTR LFYMVRAQAW SQDMAEDRRS LLHLSSRLNG ALRQEQNFAD RFLPDDEAAQ AL GKTCWEA LVSPVVQNIT SPDEDGISPL GWLLDQYLEC QEAVFNPQSR GPAFFSRVRR LTHLLVHVEP CEAPPPVVAT PRP KGRNRS HDWSSLATRG LPSSIMRNLT RCWRAVVEKQ VNNFLTSSWR DDDFVPRYCE HFNILQNSSS ELFGPRAAFL LALQ NGCAG ALLKLPFLKA AHVSEQFARH IDQQIQGSRI GGAQEMERLA QLQQCLQAVL IFSGLEIATT FEHYYQHYMA DRLLG VVSS WLEGAVLEQI GPCFPNRLPQ QMLQSLSTSK ELQRQFHVYQ LQQLDQELLK LEDTEKKIQV GLGASGKEHK SEKEEE AGA AAVVDVAEGE EEEEENEDLY YEGAMPEVSV LVLSRHSWPV ASICHTLNPR TCLPSYLRGT LNRYSNFYNK SQSHPAL ER GSQRRLQWTW LGWAELQFGN QTLHVSTVQM WLLLYLNDLK AVSVESLLAF SGLSADMLNQ AIGPLTSSRG PLDLHEQK D IPGGVLKIRD GSKEPRSRWD IVRLIPPQTY LQAEGEDGQN LEKRRNLLNC LIVRILKAHG DEGLHIDQLV CLVLEAWQK GPCPPRGLVS SLGKGSACSS TDVLSCILHL LGKGTLRRHD DRPQVLSYAV PVTVMEPHTE SLNPGSSGPN PPLTFHTLQI RSRGVPYAS CTATQSFSTF R

UniProtKB: Cullin-7

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Macromolecule #2: F-box/WD repeat-containing protein 8

MacromoleculeName: F-box/WD repeat-containing protein 8 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.628852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPMDDYSLDE FRRRWQEELA QAQAPKKRRR PEAAERRARR PEVGSGRGEQ ASGDPALAQR LLEGAGRPPA ARATRAEGQD VASRSRSPL AREGAGGGEQ LVDQLIRDLN EMNDVPFFDI QLPYELAINI FQYLDRKELG RCAQVSKTWK VIAEDEVLWY R LCQQEGHL ...String:
GPMDDYSLDE FRRRWQEELA QAQAPKKRRR PEAAERRARR PEVGSGRGEQ ASGDPALAQR LLEGAGRPPA ARATRAEGQD VASRSRSPL AREGAGGGEQ LVDQLIRDLN EMNDVPFFDI QLPYELAINI FQYLDRKELG RCAQVSKTWK VIAEDEVLWY R LCQQEGHL PDSSISDYSC WKLIFQECRA KEHMLRTNWK NRKGAVSELE HVPDTVLCDV HSHDGVVIAG YTSGDVRVWD TR TWDYVAP FLESEDEEDE PGMQPNVSFV RINSSLAVAA YEDGFLNIWD LRTGKYPVHR FEHDARIQAL ALSQDDATVA TAS AFDVVM LSPNEEGYWQ IAAEFEVPKL VQYLEIVPET RRYPVAVAAA GDLMYLLKAE DSARTLLYAH GPPVTCLDVS ANQV AFGVQ GLGWVYEGSK ILVYSLEAGR RLLKLGNVLR DFTCVNLSDS PPNLMVSGNM DGRVRIHDLR SGNIALSLSA HQLRV SAVQ MDDWKIVSGG EEGLVSVWDY RMNQKLWEVY SGHPVQHISF SSHSLITANV PYQTVMRNAD LDSFTTHRRH RGLIRA YEF AVDQLAFQSP LPVCRSSCDA MATHYYDLAL AFPYNHV

UniProtKB: F-box/WD repeat-containing protein 8

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Macromolecule #3: E3 ubiquitin-protein ligase RBX1

MacromoleculeName: E3 ubiquitin-protein ligase RBX1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.289977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MAAAMDVDTP SGTNSGAGKK RFEVKKWNAV ALWAWDIVVD NCAICRNHIM DLCIECQANQ ASATSEECTV AWGVCNHAFH FHCISRWLK TRQVCPLDNR EWEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #4: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.679965 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MPSIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.56 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 355547
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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